R Basics

Rüçhan Eker, Jean Monlong, Margot Zahm

Why R?

Why R?

Simple

  • Interpretative language (no compilation needed)
  • No manual memory management
  • Vectorized

Free

  • Widely used, vast community of R users
  • Good life expectancy

Why R?

Flexible

  • Open-source: anyone can see/create/modify
  • Multiplatform: Windows, Mac, Unix… It works everywhere

Trendy

  • More and more packages
  • More and more popular among data scientists and (now) biologists

Workshop Setup

  • Open

Workshop Setup

  • Open

Logo

Workshop Setup

Open a new R script file (File > New File > R Script)

Workshop Setup

Console

  • Where R is running
  • You can write and run the commands directly here
  • Your command executes when you press Enter

Workshop Setup

Console

Script

  • A text file with commands. Extension .R
  • To keep a trace of your analysis
  • Highly recommended
  • Run commands from a script to the console with Run button

Workshop Setup

Console

Script

Tracking panel

  • List all variables you generated
  • An history of the commands you ran

Workshop Setup

Console

Script

Tracking panel

Multipurpose panel

Check files in your computer, see plots, manage packages, read help section of a function.

Workshop Setup

Console

Script

Tracking panel

Multipurpose panel

Caution

Write everything you do in scripts to avoid loosing your work.

When you get an error

  1. Read the command, look for typos
  2. Read the error message
    1. and 2. again
  4. Raise your hand, someone will assist you

Tip

Solving errors is an important skill to learn.

Objects

Objects - Overview

Unit type

  • numeric e.g. numbers
[1] 0.1
[1] 42
[1] -1e+07
  • logical Binary two possible values
[1] TRUE
[1] FALSE
  • character e.g. words between "
[1] "male"
[1] "ENSG007"
[1] "Allez les bleus"
  • comment: line starting by #
# This is a comment line
# I can write everythin I want

Tip

Comment your script to help you remember what you have done.

Objects - Overview

Complex type

  • vector: Ordered collection of elements of the same type
[1] 1 3 5 7 9
  • list: Flexible container, mixed type possible. Recursive
$name
[1] "John Doe"

$age
[1] "40"

$skills
[1] "sing"  "dance" "run"  

$glasses
[1] FALSE

Objects - Overview

Complex type

  • matrix: Table of elements of the same type
     [,1] [,2] [,3]
[1,]    1    3    5
[2,]    2    4    6
     [,1]    [,2] [,3]
[1,] "one"   "1"  "4" 
[2,] "two"   "2"  "5" 
[3,] "three" "3"  "6"
  • data.frame: Table of mixed type elements
  Name Age IsStudent
1 John  25      TRUE
2 Jane  30     FALSE

Note

These are the basic complex types. It exists a lot of different complex objects which mix all these basic objects.

Objects - Naming conventions

  • Use letters, numbers, dot or underline characters
  • Start with letter or the dot not followed by a number
  • Some names are forbidden (ex. if, else, TRUE, FALSE)
  • Correct: valid.name, valid_name, valid2name3
  • Incorrect: valid name, valid-name, 1valid2name3

Tip

Avoid random names such as var1, var2. Use significant names: gene_list, nb_elements

Objects - Assign a value

The name of the object followed by the assignment symbol and the value.

valid.name_123 = 2
valid.name_123
[1] 2
valid.name_123 <- 2
valid.name_123
[1] 2
valid.name_123 = 4
valid.name_123
[1] 4

Objects - Arithmetic operators

You can use operators on objects to modify them. Depending on the object format, operators have different behaviors and some are forbidden.

  • addition: +
  • substraction: -
  • multiplication: *
  • division: /
  • exponent: ^ or **
  • integer division: %/%
  • modulo: %%
2+3
[1] 5
5-2
[1] 3
4*3
[1] 12
10/2
[1] 5
2^3
[1] 8
10%/%3
[1] 3
10%%3
[1] 1

Objects - Arithmetic operators

Exercise

  1. Create a numeric object
  2. Multiply it by 6
  3. Add 21
  4. Divide it by 3
  5. Substract 1
  6. Halve it
  7. Substract its original value

Objects - Arithmetic operators

Correction

my_number = 42
my_new_number = my_number * 6
my_new_number = my_new_number + 21
my_new_number = my_new_number / 3
my_new_number = my_new_number - 1
my_new_number = my_new_number / 2
my_new_number = my_new_number - my_number
my_new_number
[1] 3

Objects - Arithmetic operators

Exercise

Try to raise errors using operators.

# "Six" * "Three"
# 10 %% 0
5/0
[1] Inf
0/0
[1] NaN
(-2) ^ (1/2)
[1] NaN
1e+308 * 10
[1] Inf
1e-308 / 10
[1] 1e-309
(2 + 3i) * (4 - 5i)
[1] 23+2i

Objects - Function

  • A function is a tool to create or modify an object
  • Format: function_name(object, parameter1 = ..., parameter2 = ...)
  • Read the help manual to know more about a function (help, ? or F1)
sqrt(9)
[1] 3
sqrt.valid.name_123 = sqrt(valid.name_123)
sqrt.valid.name_123
[1] 2
help(sqrt)
?sqrt

Note

Some functions are in the default installation of R. Other functions come from packages. You can also create your own functions.

Vectors

Vectors

vector construction

  • c() Concatenate function
  • 1:10 Vector with numbers from 1 to 10
luckyNumbers = c(4,8,15,16,23,42)
luckyNumbers
[1]  4  8 15 16 23 42
oneToTen = 1:10
oneToTen
 [1]  1  2  3  4  5  6  7  8  9 10
tenOnes = rep(1,10)
tenOnes
 [1] 1 1 1 1 1 1 1 1 1 1
samples = c("sampA", "sampB")
samples
[1] "sampA" "sampB"

Vectors

vector construction

  • c() Concatenate function
  • 1:10 Vector with numbers from 1 to 10

Extra

  • seq Create a sequence of numbers
  • rep Repeat elements several times
  • runif Simulate random numbers from Uniform distribution. Same for rnorm, rpois…

Exercise - Create some vectors

Instructions

  • Create a vector withe 7 numeric values
  • Create a vector with 7 character values

Vectors

Manipulation

Using index/position between []

Characterization

  • length() Number of elements in the vector
  • names() Get or set the names of the vector’s value
luckyNumbers[3]
[1] 15
luckyNumbers[2:4]
[1]  8 15 16
luckyNumbers[2:4] = c(14,3,9)
luckyNumbers
[1]  4 14  3  9 23 42
length(luckyNumbers)
[1] 6
names(luckyNumbers)
NULL
names(luckyNumbers) = c("frank", "henry", "philip", "steve", "tom", "francis")
names(luckyNumbers)
[1] "frank"   "henry"   "philip"  "steve"   "tom"     "francis"
luckyNumbers["philip"]
philip 
     3

Vectors

Manipulation

  • sort() Sort a vector
  • sample() Shuffle a vector
  • rev() Reverse a vector
luckyNumbers
  frank   henry  philip   steve     tom francis 
      4      14       3       9      23      42 
sort(luckyNumbers)
 philip   frank   steve   henry     tom francis 
      3       4       9      14      23      42 
sort(c(luckyNumbers, 1:10))
                 philip           frank                                         
      1       2       3       3       4       4       5       6       7       8 
  steve                   henry     tom francis 
      9       9      10      14      23      42 
rev(luckyNumbers)
francis     tom   steve  philip   henry   frank 
     42      23       9       3      14       4 
sample(1:10)
 [1]  2  9  1  8  5 10  4  7  3  6

Extra

  • sort()/sample() Explore extra parameters
  • order() Get the index of the sorted elements

Vectors

Exploration

  • head()/tail() Print the first/last values
  • summary() Summary statistics
  • min()/max()/mean()/median()/var() Minimum, maximum, average, median, variance
  • sum Sum of the vector’s values
head(samples)
[1] "sampA" "sampB"
summary(luckyNumbers)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   3.00    5.25   11.50   15.83   20.75   42.00 
mean(luckyNumbers)
[1] 15.83333
min(luckyNumbers)
[1] 3

Extra

  • log/log2/log10 Logarithm functions
  • sqrt Square-root function

Vectors

Arithmetic operators

  • Simple arithmetic operations over all the values of the vector
  • Or values by values when using vectors of same length
  • Arithmetic operations: +, -, *, /
  • Other exist but let’s forget about them for now
luckyNumbers + 2
  frank   henry  philip   steve     tom francis 
      6      16       5      11      25      44 
luckyNumbers * 4
  frank   henry  philip   steve     tom francis 
     16      56      12      36      92     168 
luckyNumbers - luckyNumbers
  frank   henry  philip   steve     tom francis 
      0       0       0       0       0       0 
luckyNumbers / 1:length(luckyNumbers)
  frank   henry  philip   steve     tom francis 
   4.00    7.00    1.00    2.25    4.60    7.00

Exercise - Guess my favorite number

Instructions

  1. Create a vector with 5 numeric values
  2. Multiply it by 6
  3. Add 21
  4. Divide it by 3
  5. Substract 1
  6. Halve it
  7. Substract its original values
my_numbers = rnorm(5)
my_favorite_number = my_numbers*6
my_favorite_number = my_favorite_number + 21
my_favorite_number = my_favorite_number / 3
my_favorite_number = my_favorite_number - 1
my_favorite_number = my_favorite_number / 2
my_favorite_number - my_numbers
[1] 3 3 3 3 3